Nils Spain, the Unicef country director for Sudan, will attend the signing ceremony in Geneva on Wednesday, while the Jem delegation will be led by Suleiman Jamous, the group's humanitarian co-ordinator, and Ahmed Hussein, Jem's spokesman.
Kastberg hailed the move as a "valuable precedent which we hope all parties to the Darfur conflict will follow".
Among key issues surrounding children in Darfur is the use of child soldiers, with all parties of the conflict having been accused of recruiting minors for combat.
'No child soldiers'
Unicef estimated late in 2008 that there were around 6,000 child soldiers in Darfur alone, with the youngest just 11 years of age, while most were aged between 15 and 17.
Anyone under 18 is considered a child under international and Sudanese law. However, in many tribal cultures, they are viewed as adults after puberty.
Dennis McNamara, the mediator of the deal, noted that under the agreement, if UN officials were to "find children in military areas, or in conflict areas, they will arrange for them to be removed".
Al Jazeera's Mohamed Adow reporting from Khartoum, said: "The details of this agreement are coming at a time of increased hostility between the Sudanese government and Jem.
"The agreement was met with anger from the country's deputy minister of information who said it was illegal and Unicef's move to sign the deal with Jem is tantamount to giving the rebel group what he termed undue legitimacy," Adow said.
But Radhika Coomaraswamy, the UN special representative for children in armed conflict, said that this was not the case.
"This is not to confer legitimacy or to recongise them as armed groups under the Geneva convention," she told Al Jazeera. "We go where there are children."
Meanwhile, the Darfur armed group has insisted that "there are no child soldiers in Jem," and that the agreement goes beyond the issue of children in conflict to the welfare of children such as education.
"The signing of this agreement does not mean that Jem has recruited child soldiers. This is not true," Hussein, the Jem spokesman, told AFP news agency.
"We are taking this as an initiative of goodwill, we want to lead and set an example," Hussein said.